Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004520.1 Hibiscus syriacus cultivar Beakdansim tig00009968_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 72616
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:8366 original size:81 final size:81
Alignment explanation
Indices: 8278--8932 Score: 968
Period size: 81 Copynumber: 8.1 Consensus size: 81
8268 ATTCCTTTAG
* * * * ** * * *
8278 TCTTTTACCCAAAGGCATTTATCCTTTCATCTAATTTACATAATTGACACATTTATGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
8343 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
8359 TCTTTTACTCAAAGGCATTTAACATTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
8424 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * *
8440 TCTTTTACGCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTCACATCTTTTTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
8505 ACATCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
8521 TCTTTTACTCAAAGGTATTTAACCATTCATCTAACTGGCATAATTGATACCTTTCGGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
8586 ACAGATAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * * *
8602 TCTTTTACTCAAAGGTATTTAACATTTCATCTGACTAGCATTATTGACGCCTTTCAGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
8667 ATAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
8683 TCTTTTACTCAAATGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTTAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
8748 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
*
8764 TCTTTTACTCAAATGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
8829 ACAGCTAGGTCATTAA
66 ACAGCTAGGCCATTAA
* * *
8845 TATTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACATCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* *
8910 ACAGCTTGGACATTAA
66 ACAGCTAGGCCATTAA
8926 TCTTTTA
1 TCTTTTA
8933 ACTTTAGAAT
Statistics
Matches: 519, Mismatches: 55, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 519 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
ACAGCTAGGCCATTAA
Found at i:9256 original size:55 final size:55
Alignment explanation
Indices: 9081--9300 Score: 268
Period size: 55 Copynumber: 4.0 Consensus size: 55
9071 CCCAACACCA
* * * * * * *
9081 ATACGGAAATTCA-CCAACTTATTATGAACTTCTTA-TATTTGTACATATATTTCCC
1 ATACGGAAATTCATAC-ACTTAGTATGAATTTCTTAGT-TTTGCACACATAGTGCCC
*
9136 ATACGGAAATTCATACACTTAGTATGAATTTCTTAG-TTTGCACACCTAGTGCCC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCC
* **
9190 ATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCTT
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCC
9245 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACAC-TCAGTGCC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAG--TTTTGCACACAT-AGTGCC
9301 ATTTGGTAAT
Statistics
Matches: 145, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
54 48 0.33
55 80 0.55
56 2 0.01
57 15 0.10
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (55 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCC
Found at i:17688 original size:124 final size:125
Alignment explanation
Indices: 17467--17721 Score: 494
Period size: 124 Copynumber: 2.0 Consensus size: 125
17457 AAATAAACAG
17467 TGACCTTCAATTGAGTTTGACCAACAATATCATAATTATTTTTTCGTCATTCTTAAAAATAAAAT
1 TGACCTTCAATTGAGTTTGACCAACAATATCATAATTATTTTTTCGTCATTCTTAAAAATAAAAT
17532 TTATCTCCATTATTTTTCTTTCTTATTTAATAATTATTGATAAAAATACATAAGATGTTT
66 TTATCTCCATTATTTTTCTTTCTTATTTAATAATTATTGATAAAAATACATAAGATGTTT
17592 TGACCTTCAATTGAGTTTGACCAACAATATCATAATTA-TTTTTCGTCATTCTTAAAAATAAAAT
1 TGACCTTCAATTGAGTTTGACCAACAATATCATAATTATTTTTTCGTCATTCTTAAAAATAAAAT
*
17656 TTATCTCCATTATTTTTCTTTCTTATTTAATAATTATTGATAAAAATCCATAAGATGTTT
66 TTATCTCCATTATTTTTCTTTCTTATTTAATAATTATTGATAAAAATACATAAGATGTTT
17716 TGACCT
1 TGACCT
17722 ACAACAAGTC
Statistics
Matches: 129, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
124 91 0.71
125 38 0.29
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.45
Consensus pattern (125 bp):
TGACCTTCAATTGAGTTTGACCAACAATATCATAATTATTTTTTCGTCATTCTTAAAAATAAAAT
TTATCTCCATTATTTTTCTTTCTTATTTAATAATTATTGATAAAAATACATAAGATGTTT
Found at i:20778 original size:20 final size:20
Alignment explanation
Indices: 20755--20796 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
20745 CTAAGTATAA
*
20755 TTTCAATATTTATTTTTTGT
1 TTTCAATATTTATTTATTGT
*
20775 TTTCAATTTTTATTTATTGT
1 TTTCAATATTTATTTATTGT
20795 TT
1 TT
20797 GCTATGACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTCAATATTTATTTATTGT
Found at i:20884 original size:21 final size:21
Alignment explanation
Indices: 20860--20924 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 21
20850 AATATTACCA
*
20860 ATGTTTGCTGTGTATTCAAGT
1 ATGTTTGATGTGTATTCAAGT
*
20881 ATGTTTGATGTGAAAAATTTCAAGT
1 ATGTTTGATGTG---TA-TTCAAGT
*
20906 ATGTTTGTTGTGTATTCAA
1 ATGTTTGATGTGTATTCAA
20925 TATTTGATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
21 16 0.44
22 1 0.03
24 1 0.03
25 18 0.50
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (21 bp):
ATGTTTGATGTGTATTCAAGT
Found at i:20952 original size:43 final size:45
Alignment explanation
Indices: 20860--20958 Score: 130
Period size: 43 Copynumber: 2.2 Consensus size: 45
20850 AATATTACCA
* * * *
20860 ATGTTTGCTGTGTATTCAAGTATGTTTGATGTGAAAAATTTCAAGT
1 ATGTTTGTTGTGTATTCAAGTA-GTTTGATCTGAAAAATCTCAAAT
*
20906 ATGTTTGTTGTGTATTCAA-TA-TTTGATCTGACAAATCTCAAAT
1 ATGTTTGTTGTGTATTCAAGTAGTTTGATCTGAAAAATCTCAAAT
20949 ATGTTTGTTG
1 ATGTTTGTTG
20959 CGAAAAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
43 28 0.58
45 2 0.04
46 18 0.38
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.45
Consensus pattern (45 bp):
ATGTTTGTTGTGTATTCAAGTAGTTTGATCTGAAAAATCTCAAAT
Found at i:23107 original size:27 final size:27
Alignment explanation
Indices: 23077--23143 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
23067 AAAATTATAG
*
23077 AAATATCTCTAAAGGGTAAAATGACC-A
1 AAATACCTCTAAAGGGT-AAATGACCTA
* * * *
23104 AAATGCCCCTAAAGTGTAAATGGCCTA
1 AAATACCTCTAAAGGGTAAATGACCTA
23131 AAATACCTCTAAA
1 AAATACCTCTAAA
23144 CCCTGGAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
26 7 0.22
27 25 0.78
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.22
Consensus pattern (27 bp):
AAATACCTCTAAAGGGTAAATGACCTA
Found at i:25703 original size:33 final size:32
Alignment explanation
Indices: 25683--25770 Score: 122
Period size: 33 Copynumber: 2.7 Consensus size: 32
25673 AAAGGATTCG
25683 ATCATATTCAATTGGTGCACCTCTAGGGTTTCA
1 ATCATATTCAATTGGTGCACCT-TAGGGTTTCA
* * *
25716 ATCATCTTCAATTGGCGCACTTCTAGGGTTTCA
1 ATCATATTCAATTGGTGCACCT-TAGGGTTTCA
*
25749 ATCATATTCAACTGGTGCACCT
1 ATCATATTCAATTGGTGCACCT
25771 CCAACTACTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (32 bp):
ATCATATTCAATTGGTGCACCTTAGGGTTTCA
Found at i:28022 original size:13 final size:12
Alignment explanation
Indices: 27980--28024 Score: 72
Period size: 12 Copynumber: 3.7 Consensus size: 12
27970 TTTCTTTTAG
27980 TTTTTAAAATAA
1 TTTTTAAAATAA
27992 TTTTTAAAATAA
1 TTTTTAAAATAA
28004 TTTTTAAAATATA
1 TTTTTAAAATA-A
*
28017 ATTTTAAA
1 TTTTTAAA
28025 GGATGTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 23 0.74
13 8 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTTTTAAAATAA
Found at i:29477 original size:13 final size:13
Alignment explanation
Indices: 29459--29483 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29449 TATTATCTAC
29459 GAATGCAAATTGT
1 GAATGCAAATTGT
29472 GAATGCAAATTG
1 GAATGCAAATTG
29484 CGTATCAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (13 bp):
GAATGCAAATTGT
Found at i:31787 original size:75 final size:76
Alignment explanation
Indices: 31636--31948 Score: 341
Period size: 75 Copynumber: 4.2 Consensus size: 76
31626 CTTAATCGGT
* * * * *
31636 TAAAATAAAAT-AGTCGCTACCTATTAAGTAAAAACTA-CTTACCGATTTGTTTGAAGGTTGCTA
1 TAAAATAAAATAAGACGCTACCTATTAAGTTAAAA-TATC-TACCGGTTTGTTTAAAGGTTACTA
31699 ATAATGTAAACGG
64 ATAATGTAAACGG
* * * *
31712 TAAAATAAAATAAG-CGCTATCTATTACGTTAAAATATCTACGGGTTTGTTTAAAGATTACTAAT
1 TAAAATAAAATAAGACGCTACCTATTAAGTTAAAATATCTACCGGTTTGTTTAAAGGTTACTAAT
*
31776 AATGTGAACGG
66 AATGTAAACGG
** * *
31787 TAAAATAAAAT-AGACAATACCTATTAAGCTAAAATATCTACCGGTTAT-TTTAAATGTTACTAA
1 TAAAATAAAATAAGACGCTACCTATTAAGTTAAAATATCTACCGGTT-TGTTTAAAGGTTACTAA
*
31850 TAATGTAAACGA
65 TAATGTAAACGG
* * ** * * * * *
31862 TAAAATAAAATAAG-TGTTGTCTATTACGTTAAACTAGCTACTGGTTTGTTTAAAGGTTAATAAT
1 TAAAATAAAATAAGACGCTACCTATTAAGTTAAAATATCTACCGGTTTGTTTAAAGGTTACTAAT
31926 AATGTAAACGG
66 AATGTAAACGG
31937 TAAAATAAAATA
1 TAAAATAAAATA
31949 GGCGTACATA
Statistics
Matches: 199, Mismatches: 32, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
74 3 0.02
75 162 0.81
76 32 0.16
77 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (76 bp):
TAAAATAAAATAAGACGCTACCTATTAAGTTAAAATATCTACCGGTTTGTTTAAAGGTTACTAAT
AATGTAAACGG
Found at i:31908 original size:150 final size:151
Alignment explanation
Indices: 31636--31949 Score: 420
Period size: 150 Copynumber: 2.1 Consensus size: 151
31626 CTTAATCGGT
* ** * *
31636 TAAAATAAAATAGTCGCTACCTATTAAGTAAAAACTACTTACCGATTTGTTTGAAGGTTGCTAAT
1 TAAAATAAAATAGACAATACCTATTAAGTAAAAACTACTTACCGATTTGTTTAAAGGTTACTAAT
* *
31701 AATGTAAACGGTAAAATAAAATAAGCGCTATCTATTACGTTAAAATATCTACGGGTTTGTTTAAA
66 AATGTAAACGATAAAATAAAATAAGCGCTATCTATTACGTTAAAATAGCTACGGGTTTGTTTAAA
* *
31766 GATTACTAATAATGTGAACGG
131 GATTAATAATAATGTAAACGG
* *
31787 TAAAATAAAATAGACAATACCTATTAAGCT-AAAA-TA-TCTACCGGTTAT-TTTAAATGTTACT
1 TAAAATAAAATAGACAATACCTATTAAG-TAAAAACTACT-TACCGATT-TGTTTAAAGGTTACT
* * * * *
31848 AATAATGTAAACGATAAAATAAAATAAGTGTTGTCTATTACGTTAAACTAGCTACTGGTTTGTTT
63 AATAATGTAAACGATAAAATAAAATAAGCGCTATCTATTACGTTAAAATAGCTACGGGTTTGTTT
*
31913 AAAGGTTAATAATAATGTAAACGG
128 AAAGATTAATAATAATGTAAACGG
31937 TAAAATAAAATAG
1 TAAAATAAAATAG
31950 GCGTACATAT
Statistics
Matches: 143, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
149 1 0.01
150 111 0.78
151 30 0.21
152 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (151 bp):
TAAAATAAAATAGACAATACCTATTAAGTAAAAACTACTTACCGATTTGTTTAAAGGTTACTAAT
AATGTAAACGATAAAATAAAATAAGCGCTATCTATTACGTTAAAATAGCTACGGGTTTGTTTAAA
GATTAATAATAATGTAAACGG
Found at i:31969 original size:22 final size:23
Alignment explanation
Indices: 31944--32014 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
31934 CGGTAAAATA
31944 AAATAGGCG-TACATATTATGTT
1 AAATAGGCGCTACATATTATGTT
* *
31966 AAATAGGTGCTACCA-ATTACGTT
1 AAATAGGCGCTA-CATATTATGTT
*
31989 AAATAAGCGCTACATATTATGTT
1 AAATAGGCGCTACATATTATGTT
32012 AAA
1 AAA
32015 CTAGCTATCG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 10 0.24
23 29 0.71
24 2 0.05
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (23 bp):
AAATAGGCGCTACATATTATGTT
Found at i:32126 original size:21 final size:20
Alignment explanation
Indices: 32098--32138 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
32088 ATTTTTTAAA
*
32098 ATTCAAAAGTATAGATACTT
1 ATTCAAAAGTATAAATACTT
32118 ATTCTAAAAGTATAAATACTT
1 ATTC-AAAAGTATAAATACTT
32139 TAAAGGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (20 bp):
ATTCAAAAGTATAAATACTT
Found at i:32260 original size:23 final size:23
Alignment explanation
Indices: 32231--32303 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
32221 CCTGAAAATA
* * *
32231 AAATAGGTGATATCTATTATGTT
1 AAATAGGCGATACCTATTACGTT
*
32254 AAATAGGCGTTACCTATTACGTT
1 AAATAGGCGATACCTATTACGTT
* *
32277 AAATAAGCGCTACCTATTACGTT
1 AAATAGGCGATACCTATTACGTT
32300 AAAT
1 AAAT
32304 TAGCTACTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Consensus pattern (23 bp):
AAATAGGCGATACCTATTACGTT
Found at i:36668 original size:34 final size:33
Alignment explanation
Indices: 36630--36696 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
36620 GTAATAAACA
36630 AAATTAAGCAAAATAAATTAACAA-AAAGTCCAAC
1 AAATTAAGCAAAATAAATTAA-AATAAA-TCCAAC
* *
36664 AAATTTATCAAAATAAATTAAAATAAATCCAAC
1 AAATTAAGCAAAATAAATTAAAATAAATCCAAC
36697 CATATTAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 8 0.27
34 22 0.73
ACGTcount: A:0.61, C:0.13, G:0.03, T:0.22
Consensus pattern (33 bp):
AAATTAAGCAAAATAAATTAAAATAAATCCAAC
Found at i:39020 original size:21 final size:20
Alignment explanation
Indices: 39000--39057 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 20
38990 CAAAAAAAAT
39000 TAATTAAATAAAATATTAAA
1 TAATTAAATAAAATATTAAA
39020 TAAATTAAATAAAAAATATTAAA
1 T-AATTAAAT--AAAATATTAAA
39043 -AA-TATAATAAAATAT
1 TAATTA-AATAAAATAT
39058 ACCTTAGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 7 0.21
20 3 0.09
21 13 0.38
23 11 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAATTAAATAAAATATTAAA
Found at i:45508 original size:26 final size:26
Alignment explanation
Indices: 45437--45510 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
45427 ATCGTTTATT
45437 TTTTAACTTT-TTAATAATAAAAAAATA
1 TTTTAA-TTTATTAATAA-AAAAAAATA
* ** *
45464 TTTTAATTAAAAAAGAAAAAAAAATA
1 TTTTAATTTATTAATAAAAAAAAATA
*
45490 TTTTAATTTATTTATAAAAAA
1 TTTTAATTTATTAATAAAAAA
45511 CCCAACTTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
26 27 0.73
27 10 0.27
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (26 bp):
TTTTAATTTATTAATAAAAAAAAATA
Found at i:50242 original size:319 final size:320
Alignment explanation
Indices: 49662--50300 Score: 1174
Period size: 319 Copynumber: 2.0 Consensus size: 320
49652 GCATTAATGT
49662 TAGAAGCAATGAAGATATGCATAGCCTTGCTTTTAGAAGGCACTGATCCCTTTATATCCTGCTTT
1 TAGAAGCAATGAAGATATGCATAGCCTTGCTTTTAGAAGGCACTGATCCCTTTATATCCTGCTTT
*
49727 CACATTGATAGTTACTGAACTAGATTGCTCAACAATCAGGGATAATGATTAAAAATTTAACAAAT
66 CACATTGATAGTTACTGAACTAGATTGCTCAACAATCAGGAATAATGATTAAAAATTTAACAAAT
* *
49792 GCTAGACTATCATCAGTTTAATTTATAGATATGAAAATCTGGAAATATGTACCTCAGTGTAGGCT
131 GCTAGACCATCATCAGTTTAATTTATAGATATGAAAATCTGGAAATATGTACCTCAGTATAGGCT
*
49857 TGCATCGAGAGCAGATAAATTCTTCACCGATTCCGAAGAACAGCGGTCATATTTCAAAATAAAAA
196 TGCATCCAGAGCAGATAAATTCTTCACCGATTCCGAAGAACAGCGGTCATATTTCAAAATAAAAA
49922 TGCATGATCATCATTTTGCAGGAATGGACTCAAGGGCGTACCGGTTAAGCTGCTTGAAAG
261 TGCATGATCATCATTTTGCAGGAATGGACTCAAGGGCGTACCGGTTAAGCTGCTTGAAAG
49982 TAGAAGCAATGAAGATATGCATAGCCTTGCTTTTAGAAGGCACTGATCCC-TT-TATCCTGCTTT
1 TAGAAGCAATGAAGATATGCATAGCCTTGCTTTTAGAAGGCACTGATCCCTTTATATCCTGCTTT
* ** *
50045 CACATTGATATTTACTTTACTAGATTGCTCAACAATCAGGAATACTGATTAAAAATTTAACAAAT
66 CACATTGATAGTTACTGAACTAGATTGCTCAACAATCAGGAATAATGATTAAAAATTTAACAAAT
50110 GCTAGACCATCATCAGTTTAATTTTATAGATATGAAAATCTGGAAATATGTACCTCAGTATAGGC
131 GCTAGACCATCATCAGTTTAA-TTTATAGATATGAAAATCTGGAAATATGTACCTCAGTATAGGC
50175 TTGCATCCAGAGCAGATAAATTCTTCACCGATTCCGAAGAACAGCGGTCATATTTCAAAATAAAA
195 TTGCATCCAGAGCAGATAAATTCTTCACCGATTCCGAAGAACAGCGGTCATATTTCAAAATAAAA
*
50240 ATGCATGATCATCATTTTGCAGGAATGGACTTAAGGGCGTACCGGTTAAGCTGCTTGAAAG
260 ATGCATGATCATCATTTTGCAGGAATGGACTCAAGGGCGTACCGGTTAAGCTGCTTGAAAG
50301 AAAGTGATGT
Statistics
Matches: 309, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
318 91 0.29
319 168 0.54
320 50 0.16
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (320 bp):
TAGAAGCAATGAAGATATGCATAGCCTTGCTTTTAGAAGGCACTGATCCCTTTATATCCTGCTTT
CACATTGATAGTTACTGAACTAGATTGCTCAACAATCAGGAATAATGATTAAAAATTTAACAAAT
GCTAGACCATCATCAGTTTAATTTATAGATATGAAAATCTGGAAATATGTACCTCAGTATAGGCT
TGCATCCAGAGCAGATAAATTCTTCACCGATTCCGAAGAACAGCGGTCATATTTCAAAATAAAAA
TGCATGATCATCATTTTGCAGGAATGGACTCAAGGGCGTACCGGTTAAGCTGCTTGAAAG
Found at i:51654 original size:13 final size:13
Alignment explanation
Indices: 51636--51671 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
51626 TACTTGAAAA
51636 AATTGAATTTTAT
1 AATTGAATTTTAT
51649 AATTGAATTTTAT
1 AATTGAATTTTAT
* *
51662 GATTCAATTT
1 AATTGAATTT
51672 GATGTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (13 bp):
AATTGAATTTTAT
Found at i:52212 original size:23 final size:23
Alignment explanation
Indices: 52177--52226 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
52167 ATGTTATCTG
52177 TCTTTATGACACGTTTATCTCTA
1 TCTTTATGACACGTTTATCTCTA
* * *
52200 TCTTTGTGGCACGTTTTTCTCTA
1 TCTTTATGACACGTTTATCTCTA
52223 -CTTT
1 TCTTT
52227 TTGGTAGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.14, C:0.22, G:0.12, T:0.52
Consensus pattern (23 bp):
TCTTTATGACACGTTTATCTCTA
Found at i:62146 original size:2 final size:2
Alignment explanation
Indices: 62139--62193 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
62129 CCTTGGTTAT
62139 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62180 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
62194 AAGTAAAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:66404 original size:15 final size:17
Alignment explanation
Indices: 66372--66404 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
66362 GTATCAATTC
66372 TGACATCTCTATGTCAA
1 TGACATCTCTATGTCAA
66389 TGACATC-CTA-GTCAA
1 TGACATCTCTATGTCAA
66404 T
1 T
66405 CAATAACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (17 bp):
TGACATCTCTATGTCAA
Done.